Not so hot on the core upgrades, since they make less "sense", where for the other stuff you could reasonably suppose to get the best parts from all of the low-quality units. Still, this also does run the risk of making pristine finds a lot less exciting. Could *possibly* be balanced with a high enough story point cost, but I don't know.)
In terms of being a story point sink, the core upgrades is
vital. You only ever truly need one pristine nanoforge, for example, but you can always use more alpha cores. (Well, okay, until you've got the entire sector colonized, I suppose?)
As for making it make lore-sense - perhaps this is something you can only do if you have an alpha core on hand already to oversee the component redistribution? Perhaps this sort of upgrade is a matter of getting the right networking together - quantum-synchronizing the lower-grade cores so they operate as a unit - much like how in the modern world, computer clusters or cloud computing have largely overtaken singular supercomputers? Maybe it even requires a specific building (Black Research Facility) that all but guarantees Pather interest - and requires heftier bribes for the Hegemony to ignore? (I'd imagine that, like the Planetary Shield Generator, this is something you'd find via quest, rather than just build. I'd also imagine that Tri-Tachyon already has one that you can use for a fee.)
Where to put the UI... that depends a bit on the requirements. If you need a Black Research Facility, then maybe that just adds a person to the local comm listings? If I were trying to mod this in, that's probably how I'd do it.
The other "obvious" option would be to add a fourth tab to custom production: ships/weapons/fighters/special, with the "special" category being for random unique stuff that frequently has non-credit costs or requirements that aren't just "has heavy industry somewhere". This would also let you tie upgrades into the blueprint system - maybe you start with the blueprint to create Beta Cores from Gamma Cores, but the rest are things you'd need to find?
The concern about making pristine nanoforge & synchrotron core finds feel less special is sensible, though, and one I don't have a good answer for. On the other hand, in my most recent game, I've taken to just selling corrupted nanoforges, since I literally have no use for them.
...Oh, a minor suggestion: if you sell a nanoforge or synchrotron core to someplace that can install it, you should get a
significant rep boost with that faction. Or, alternatively, there should be a way to hand one over to the local administration, similar to the 'hand in AI cores' option.
Suggestion: If Hammerhead (with free ITU) start stays in the next release, I suggest it gets ITU built-in for free.
(You could build it in yourself. If I'm going to go customizing these starting variants, I'll probably just remove the ITU from it since that'd make more sense, imo 
)
I really like the hammerhead start with ITU; it feels storied in a way that the other starts (aside from Spacer) don't. Here's this ship that you could not possibly have outfitted yourself. Where did you get it? Perhaps it was a decommissioned military vessel that you burned bridges acquiring as part of a retirement package. Maybe it's an ancient hand-me-down from your mother, and from her mother, and so on back for generations, which has been refit and retuned so many times by so many different people that it's no surprise it's above stock specifications. Maybe it was a lucky find at a tech mining site, that you kept quiet about until you could round up a crew to get this completely pristine domain-era warship off planet under your command.
